I am new LEfSe and bioinformatics in general, but I have successfully run the analysis with conda. However, looking through the tutorials (apologies if I missed it) I couldn’t find a way to see a table with taxa and associated LDA scores. So is there a way to export such table to a .tsv file?
Looking at the usage options from lefse_run.py I saw -o str (set the file for exporting the result (only concise textual form)) as a command. Could someone please give an example on how to use this. I tried the code below and did not run.
lefse_run.py pre_posthurricane.LEfSe.in pre_posthurricane.LEfSe.res